MetaBar - a tool for consistent contextual data acquisition and standards compliant submission

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Hankeln, Wolfgang ^a,b   Buttigieg, Pier L ^a,b   Fink, Dennis ^a   Kottmann, Renzo ^a   Yilmaz, Pelin ^a,b   Glöckner, Frank O ^a,b  

^a MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

^b JACOBS UNIVERSITY BREMEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ECOLOGICAL GENOMICS; ELECTRONIC STORAGE; EUROPEAN MOLECULAR BIOLOGY LABORATORIES; GNU GENERAL PUBLIC LICENSE; INTERNATIONAL NUCLEOTIDE SEQUENCE DATABASE; MANAGEMENT CAPABILITIES; UNIQUE IDENTIFIERS; WEB-BASED SOFTWARES;

DATA ACQUISITION; DATA VISUALIZATION; ECOLOGY; GENES; METADATA; OPEN SYSTEMS; PROJECT MANAGEMENT; SPREADSHEETS;

REGULATORY COMPLIANCE;

ARTICLE; COMPUTER INTERFACE; COMPUTER LANGUAGE; COMPUTER PROGRAM; GENETIC DATABASE; GENOMICS; INFORMATION RETRIEVAL; INTERNET; METHODOLOGY; NUCLEOTIDE SEQUENCE; SYSTEM ANALYSIS;

BASE SEQUENCE; DATABASES, GENETIC; GENOMICS; INFORMATION STORAGE AND RETRIEVAL; INTERNET; PROGRAMMING LANGUAGES; SOFTWARE; USER-COMPUTER INTERFACE; WORKFLOW;

EID: 77954055630     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-358     Document Type: Article

References (21)

1. Hall N. Advanced sequencing technologies and their wider impact in microbiology. J Exp Biol 2007, 210:1518-1525. 10.1242/jeb.001370, 17449817.
2. Field D, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008, 26:541-547. 10.1038/nbt1360, 2409278, 18464787.
3. Wieczorek J. The point-radius method for georeferencing locality descriptions and calculating associated uncertainty. International journal of geographical information science 2004, 18:745-767.
4. DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, Frigaard N-U, Martinez A, Sullivan MB, Edwards R, Brito BR, Chisholm SW, Karl DM. Community genomics among stratified microbial assemblages in the ocean's interior. Science 2006, 311:496-503. 10.1126/science.1120250, 16439655.
5. Janies D, Hill AW, Guralnick R, Habib F, Waltari E, Wheeler WC. Genomic analysis and geographic visualization of the spread of avian influenza (H5N1). Syst Biol 2007, 56:321-329. 10.1080/10635150701266848, 17464886.
6. Ramette A. Multivariate analyses in microbial ecology. FEMS Microbiol Ecol 2007, 62:142-160. 10.1111/j.1574-6941.2007.00375.x, 2121141, 17892477.
7. Fuhrman JA, Hewson I, Schwalbach MS, Steele JA, Brown MV, Naeem S. Annually reoccurring bacterial communities are predictable from ocean conditions. Proc Natl Acad Sci USA 2006, 103:13104-13109. 10.1073/pnas.0602399103, 1559760, 16938845.
8. Pommier T, Canbäck B, Riemann L, Boström KH, Simu K, Lundberg P, Tunlid A, Hagström A. Global patterns of diversity and community structure in marine bacterioplankton. Mol Ecol 2007, 16:867-880. 10.1111/j.1365-294X.2006.03189.x, 17284217.
9. Parks DH, Porter M, Churcher S, Wang S, Blouin C, Whalley J, Brooks S, Beiko R. GenGIS: A geospatial information system for genomic data. Genome Res 2009, 10:1896-1904.
10. Green JL, Bohannan BJM, Whitaker RJ. Microbial biogeography: from taxonomy to traits. Science 2008, 320:1039-1043. 10.1126/science.1153475, 18497288.
11. Schriml LM, Arze C, Nadendla S, Ganapathy A, Felix V, Mahurkar A, Phillippy K, Gussman A, Angiuoli S, Ghedin E, White O, Hall N. GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database. Nucleic Acids Res 2009, 38:D754-D764. 10.1093/nar/gkp832, 2808878, 19850722.
12. Field D. Working together to put molecules on the map. Nature 2008, 453:978. 10.1038/453978b, 18563126.
13. Consortium, U The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res 2010, 38:D142-D148. 10.1093/nar/gkp846, 2808944, 19843607, Consortium, U.
14. Howe D, Costanzo M, Fey P, Gojobori T, Hannick L, Hide W, Hill D, Kania PR, Schaeffer M, Pierre SS, Twigger S, White O, Rhee SY. Big data: The future of biocuration. Nature 2008, 455:47-50. 10.1038/455047a, 2819144, 18769432.
15. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glöckner FO. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 2007, 35:7188-7196. 10.1093/nar/gkm864, 2175337, 17947321.
16. Cole JR, Chai B, Farris RJ, Wang Q, Kulam SA, McGarrell DM, Garrity GM, Tiedje JM. The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res 2005, 33:D294-D296. 10.1093/nar/gki038, 539992, 15608200.
17. Liolios K, Chen IMA, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2009, 38:D346-D354. 10.1093/nar/gkp848, 2808860, 19914934.
18. Kottmann R, Kostadinov I, Duhaime MB, Buttigieg PL, Yilmaz P, Hankeln W, Waldmann J, Glöckner FO. Megx.net: integrated database resource for marine ecological genomics. Nucleic Acids Res 2009, 38:D391-D395. 10.1093/nar/gkp918, 2808895, 19858098.
19. Kottmann R, Gray T, Murphy S, Kagan L, Kravitz S, Lombardot T, Field D, Glöckner FO, Consortium GS. A standard MIGS/MIMS compliant XML Schema: toward the development of the Genomic Contextual Data Markup Language (GCDML). OMICS 2008, 12:115-121. 10.1089/omi.2008.0A10, 18479204.
20. Booth T, Gilbert J, Neufeld JD, Ball J, Thurston M, Chipman K, Joint I, Field D. Handlebar: a flexible, web-based inventory manager for handling barcoded samples. Biotechniques 2007, 42:300-302. 10.2144/000112385, 17390536.
21. Ratnasingham S, Hebert PDN. bold: The Barcode of Life Data System. Mol Ecol Notes 2007, 7:355-364. 10.1111/j.1471-8286.2007.01678.x, 1890991, 18784790., http://www.barcodinglife.org